Decentralised wastewater treatment systems offer an opportunity to introduce wastewater treatment and generate irrigation water in places that are not connected to centralised treatment plants. The advantages of decentralised technologies include their capability to provide wastewater treatment infrastructure in remote and hilly rural communities and their flexible adaptation to fast-growing semi-urban settlements. In this study we investigate the costs and benefits of introducing decentralised wastewater treatment and re-use to two locations in Jordan. The cost–benefit analysis (CBA) used here differs from traditional CBA in that it includes non-market benefits for which monetary values are not readily available, in addition to market benefits. We elaborate on three valuation methods to monetise benefits associated with the environment, health and irrigation in agriculture. Our findings suggest that it is principally worthwhile to establish decentralised treatment technologies in remote areas.